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Primerize PCR Assembly Design Server

⚠️ This server has been decommissioned (May 2026). The AWS EC2 instance has been terminated. See Migration below for the current site and archive details.

Primerize Logo

This is the Source Code repository for Primerize PCR Primer Assembly Design Server. The production server was freely accessible at https://primerize.stanford.edu/.

Migration

In May 2026, primerize.stanford.edu was migrated from this Django/MySQL AWS server to a static GitHub Pages site.

Details
New site https://primerize.stanford.edu/ (GitHub Pages)
New site repo https://github.com/DasLab/primerize.github.io
Primerize package https://github.com/ribokit/Primerize (v2.0.0, Python 3)
Archive DasLab Shared Drive → Projects → AWS Server Archives → Primerize_2026/
Archive contents primerize_aws_archive.tar.gz (Django app), primerize_db.sql (MySQL dump), README.docx
AMI snapshot primerize-aws-final-2026-05 (us-west-2)

To run the old site locally from the archive, see README.docx in the Google Drive folder above.

Installation

Primerize Server requires the following Python packages as dependencies, most of which can be installed through pip.

boto >= 2.38.0
Django >= 1.9.1
django-adminplus >= 0.5
django-crontab >= 0.7.0
django-environ >= 0.4.0
django-filemanager == 0.0.2
django-suit >= 0.2.15
django-widget-tweaks >= 1.4.1
gviz-api.py == 1.8.2
MySQL-python >= 1.2.5
PyGithub >= 1.26.0
pytz >= 2015.7
requests >= 2.9.1
simplejson >= 3.8.1

primerize >= 1.1.0

The primerize package is available internally at Primerize.

The gviz-api.py is available at google-visualization-python.

The django-filemanager is a modified version of django-filemanager. The source code is available internally at this fork.

Install with:

cd ~
git clone https://github.com/ribokit/Primerize.git
cd Primerize
sudo python setup.py install

cd ..
git clone https://github.com/google/google-visualization-python.git
cd google-visualization-python
sudo python setup.py install

cd ..
git clone https://github.com/t47io/django-filemanager.git
cd django-filemanager
sudo python setup.py install

Primerize Server also requires proper setup of llvm, mysql.server, apache2, mod_wsgi, openssl, gdrive, awscli, and cron jobs.

Lastly, assets preparation is required for the 1st time through running sudo python manage.py versions, sudo python manage.py dist, util_prep_dir.sh, util_src_dist.sh, util_minify.sh, util_chmod.sh and manually replacing config/*.conf. For full configuration, please refer to Documentation.

Usage

To run the test/dev server, use:

cd path/to/server_primerize/repo
python manage.py runserver

The server should be running at localhost:8000 with a python session interactive in terminal.

Documentation

  • Documentation is available at admin manual and reference.

  • Alternatively, read the repository Wiki.

License

Copyright © 2014-2017: Siqi Tian [t47], Das Lab, Stanford University. All Rights Reserved.

Primerize Server Source Code is proprietary and confidential. Unauthorized copying of this repository, via any medium, is strictly prohibited.

Copyright © of Primerize Source Code is described in LICENSE.md.

Reference

Tian, S., et al. (2015)
Primerize: Automated Primer Assembly for Transcribing Interesting RNAs.
Nucleic Acid Research 43 (W1): W522-W526.

Tian, S., and Das, R. (2017)
Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
Bioinformatics 33 (9): 1405-1406.

by t47, August 2016.